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Forum: Sample Prep / Library Generation 10-28-2018, 04:57 AM
Replies: 0
Views: 897
Posted By vanillasky
RNA on a DNA High senstivity chip

I am trying to determine if my DNAse I digest worked and I only have total RNA present in sample (for transcriptomic analysis). This sample was cleaned after the digest. I'm not sure what I am seeing...
Forum: Bioinformatics 06-02-2015, 05:49 AM
Replies: 0
Views: 844
Posted By vanillasky
MG-RAST heatmaps vs tables

Hi,

I loaded different metagenomes and
compared them using the heatmap at the gene function level (the highest
level of comparison). I then downloaded the
values associated with the heatmap. I...
Forum: Bioinformatics 05-17-2015, 11:21 AM
Replies: 0
Views: 1,448
Posted By vanillasky
Question Reliability of short read annotations

Hi,

I would like to know how reliable annotations are for metagenome short reads generated by illumina sequencing ~70-100bp when reads are annotated for function (i.e. via MG-RAST, MEGAN etc)?...
Forum: Bioinformatics 03-02-2015, 08:16 AM
Replies: 0
Views: 1,433
Posted By vanillasky
Low number of Blastp Outputs for predicted ORFs

I recently tried to annotate two assembled metagenome samples derived from the same sample type (both samples come from the same type of material) using blastp and the metagene gene predictor tool...
Forum: Bioinformatics 02-04-2015, 09:27 AM
Replies: 5
Views: 2,697
Posted By vanillasky
I used Velvet and Metavelvet to do the assemblies...

I used Velvet and Metavelvet to do the assemblies and kmergenie to find the coverage cut-off to use in the assembly. There were about 12 million reads that went into the assembly. My reads had...
Forum: Bioinformatics 02-03-2015, 03:57 AM
Replies: 5
Views: 2,697
Posted By vanillasky
Thank you for your response. In this case I know...

Thank you for your response. In this case I know from the short read information that the sample is very diverse with many genes (x,y, z etc) with different functional roles and one set of genes with...
Forum: Bioinformatics 01-30-2015, 04:03 AM
Replies: 5
Views: 2,697
Posted By vanillasky
Assembled contigs vs short reads

I have recently finished assembling some metagenome sequences and after assigning function to my contigs I see that most genes belong to three specific types of microorganisms. I also submitted the...
Forum: Bioinformatics 01-22-2015, 09:34 PM
Replies: 5
Views: 1,777
Posted By vanillasky
Cut-off values

Thank you for your suggestion. However, my question is a fundamental one. How does one decide on a cut-off value (s) with which to filter out the blasp results? For example based on greatest %...
Forum: Bioinformatics 01-22-2015, 07:09 AM
Replies: 5
Views: 1,777
Posted By vanillasky
Smile Blastp for identifying genes in contigs

I have used NCBI blastp as a first step to identify predicted ORFs in my assembled contigs. My question is how to filter these results based on % identity of the protein and e-value scores. I picked...
Forum: Illumina/Solexa 07-24-2014, 10:36 AM
Replies: 4
Views: 1,507
Posted By vanillasky
Hi GenoMax, I actually obtain similar...

Hi GenoMax,

I actually obtain similar results using other assembly programs such as velvet for example. Why would a high number of reads in general not match up with a set of contigs post assembly?
Forum: Illumina/Solexa 07-24-2014, 07:02 AM
Replies: 4
Views: 1,507
Posted By vanillasky
CLC-Reads do not map back to contigs

I have been using CLC genomics to try and assemble paired end reads from an illumina run (this is an environmental metagenome sample). The assembly is set up so that at the end, the reads are mapped...
Forum: De novo discovery 07-03-2014, 01:26 AM
Replies: 1
Views: 1,621
Posted By vanillasky
Assess an illumina metagenome assembly

I've just finished my first shot at assembling a metagenome sample derived from a marine environment using Velvet, VelvetOptimizer and Metavelvet. Running the assembly with the recommendations from...
Forum: Bioinformatics 07-03-2014, 01:13 AM
Replies: 3
Views: 1,012
Posted By vanillasky
What other options are there besides the web...

What other options are there besides the web based tools? Are the stand alone programs more advantageous?
Forum: Bioinformatics 07-02-2014, 11:03 AM
Replies: 123
Views: 46,101
Posted By vanillasky
Request for Tablet Tutorial

Hi,

I'm trying to use Tablet to visualize a metagenome assembly. I wanted to ask what the mismatch feature is and how it can be used as it was not discussed in your paper. Is there anyway you...
Forum: Bioinformatics 07-02-2014, 05:54 AM
Replies: 3
Views: 1,012
Posted By vanillasky
Analyzing metagenomic contigs

I have just finished running an assembly with Metavelvet and now have the contig file. Since I am new to the assembly process I wanted to ask what programs can be used next to analyze these contigs?
Forum: Sample Prep / Library Generation 06-19-2014, 10:17 PM
Replies: 2
Views: 4,013
Posted By vanillasky
Thank you for the reply. Unfortunately, I did end...

Thank you for the reply. Unfortunately, I did end up sequencing and found that there were contaminants in there. I was never able to get this particular sample to work with the library preparation...
Forum: Bioinformatics 05-15-2014, 05:48 AM
Replies: 17
Views: 4,313
Posted By vanillasky
So after one week of running, the output was...

So after one week of running, the output was really awful, with an N50 of 1 and the coverage was estimated as 6. Can you give me any input on how to better pick the kmer size? The output I get now...
Forum: Bioinformatics 05-09-2014, 04:59 AM
Replies: 17
Views: 4,313
Posted By vanillasky
I used kmer genie http://kmergenie.bx.psu.edu/

I used kmer genie http://kmergenie.bx.psu.edu/
Forum: Bioinformatics 05-09-2014, 03:57 AM
Replies: 17
Views: 4,313
Posted By vanillasky
Hi mastal, Thanks for the feedback. I have...

Hi mastal,

Thanks for the feedback. I have 1TB of diskspace so I think the output dir should have enough room. I turned on the scaffolding because I plan on using metavelvet next and it requires...
Forum: Bioinformatics 05-09-2014, 12:10 AM
Replies: 17
Views: 4,313
Posted By vanillasky
In response to mastal: I used up all 250 GBi when...

In response to mastal: I used up all 250 GBi when I tried to run a sequence file of 2.3 GB and the program was killed after two days. I am now trying a smaller sequence file 390MB and while the...
Forum: Bioinformatics 05-09-2014, 12:05 AM
Replies: 17
Views: 4,313
Posted By vanillasky
The script I am running is: ./velvetg...

The script I am running is:

./velvetg /home/vanillasky/genomes/outdir -exp_cov auto -cov_cutoff auto -scaffolding yes -min_contig_lgth 250 -amos_file yes
Forum: Bioinformatics 05-08-2014, 05:07 AM
Replies: 17
Views: 4,313
Posted By vanillasky
But if the distribution of kmers for my sequences...

But if the distribution of kmers for my sequences show that kmer of 13 is best why would I use a higher kmer? How will this effect the output in the end? What happens when you use a kmer size that is...
Forum: Bioinformatics 05-08-2014, 12:34 AM
Replies: 4
Views: 1,558
Posted By vanillasky
Hi Lac302! Maybe you can clarify what you mean by...

Hi Lac302! Maybe you can clarify what you mean by mining assemblies? I am interested in annotating the contigs coming out of my assembled metagenomes. Ultimately, yes I would like to focus on those...
Forum: Bioinformatics 05-07-2014, 05:23 AM
Replies: 17
Views: 4,313
Posted By vanillasky
The output I get is: Copyright 2007, 2008...

The output I get is:

Copyright 2007, 2008 Daniel Zerbino (zerbino@ebi.ac.uk)
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or...
Forum: Bioinformatics 05-07-2014, 05:07 AM
Replies: 17
Views: 4,313
Posted By vanillasky
I assume it gets killed because I run out of RAM...

I assume it gets killed because I run out of RAM (slowly filled up overtime). There is no error message and there are no output files before the program is killed. I am using a short kmer size...
Showing results 1 to 25 of 42

 


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